Gradio 案例——将 dicom 文件转为 nii文件

• 利用 SimpleITK 库，将 dicom 文件转为 nii文件
• 更完整、丰富的示例项目见 GitHub - AlionSSS/dcm2niix-webui: The web UI for dcm2niix (DICOM to NIfTI converter)

界面截图

依赖安装

• 新建一个虚拟环境 Python 3.9.16
• 依赖
  • $ pip install gradio==4.29 -i "https://pypi.doubanio.com/simple/"
  • $ pip install SimpleITK==2.3.1 -i "https://pypi.doubanio.com/simple/"

项目目录结构

dicom2nii-webui       # 目录
--/lib_SimpleITK.py   # py文件
--/main.py            # py文件，入口

代码

• lib_SimpleITK.py

import SimpleITK as sitk
import os


def dicom_to_nii(dicom_dir_path: str, nii_file_path: str):
    """
    dicom文件转nii文件
    """
    # 读取 dicom
    reader = sitk.ImageSeriesReader()
    img_name = reader.GetGDCMSeriesFileNames(dicom_dir_path)
    reader.SetFileNames(img_name)
    image = reader.Execute()
    # 转为 nii.gz
    image_array = sitk.GetArrayFromImage(image)
    image_out = sitk.GetImageFromArray(image_array)
    image_out.SetOrigin(image.GetOrigin())
    image_out.SetSpacing(image.GetSpacing())
    image_out.SetDirection(image.GetDirection())
    # 保存nii.gz文件到配置的目录下
    example_nii_dir_path = os.path.dirname(nii_file_path)
    if not os.path.exists(example_nii_dir_path) or not os.path.isdir(example_nii_dir_path):
        os.mkdir(example_nii_dir_path)
    sitk.WriteImage(image, nii_file_path)

• main.py

import gradio as gr
import os
import zipfile
import lib_SimpleITK

example_dicom_dir_path = 'D:/project/xxx/Task/ABC_Test_02/xxx'
example_nii_file_path = 'D:/project/res/result_image.nii.gz'

def service_local_dicom_to_nii(dicom_dir_path: str, nii_file_path: str):
    # 校验
    if not dicom_dir_path or dicom_dir_path.strip() == "":
        gr.Warning(f"请填入[dicom文件目录路径]，例如'{example_dicom_dir_path}'")
        return
    if not nii_file_path or nii_file_path.strip() == "":
        nii_file_path = os.path.join(dicom_dir_path, "result_image.nii.gz")

    try:
        lib_SimpleITK.dicom_to_nii(os.path.abspath(dicom_dir_path), os.path.abspath(nii_file_path))
    except Exception as e:
        raise gr.Error("dicom 转 nii 时，发生异常：" + str(e))
        
    return nii_file_path, nii_file_path 

    
local_iface = gr.Interface(
    fn=service_local_dicom_to_nii,
    inputs=[
        gr.Textbox(label="dicom文件目录路径", info=f"例如'{example_dicom_dir_path}'"),
        gr.Textbox(label="生成的nii文件路径", info=f"例如'{example_nii_file_path}'。如果不填，会输出到dicom目录下。")
    ],
    outputs=[gr.Textbox(label="生成的nii文件路径"), gr.File(label="生成的nii文件")],
    description="在本地电脑端启动时使用。利用 SimpleITK 库，将 dicom 文件转为 nii文件。",
)

def unzip_file(zip_file_path: str, save_dir_path: str):
    with zipfile.ZipFile(zip_file_path, "r") as zfile:
        # 中文有乱码问题
        zfile.extractall(save_dir_path)

def service_server_dicom_to_nii(file):
    # 解压
    save_dir_path = os.path.dirname(file.name)
    print(save_dir_path)
    unzip_file(file.name, save_dir_path)
    
    # dicom 转 nii
    dicom_dir_path = save_dir_path
    nii_file_path = os.path.join(save_dir_path, "result_image.nii.gz") 
    try:
        lib_SimpleITK.dicom_to_nii(dicom_dir_path, nii_file_path)
    except Exception as e:
        raise gr.Error("dicom 转 nii 时，发生异常：" + str(e))
        
    # return nii_file_path, nii_file_path
    return file.name, file.name 

server_iface = gr.Interface(
    fn=service_server_dicom_to_nii,
    inputs=[gr.File(label="dicom文件目录的压缩包（建议不要带中文）")],
    outputs=[gr.Textbox(label="生成的nii文件路径"), gr.File(label="生成的nii文件")],
    description="在服务器端启动时使用。利用 SimpleITK 库，将 dicom 文件转为 nii文件。",
)


tabbed_interface = gr.TabbedInterface(
    interface_list = [local_iface, server_iface], 
    tab_names = ["本地端", "通用端"],
    title="dicom 转 nii"
)
tabbed_interface.launch()